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Advances in next-generation sequencing technology have enabled the high-throughput profiling of metagenomes and accelerated the microbiome study. Recently, there has been a rise in quantitative studies that aim to decipher the microbiome co-occurrence network and its underlying community structure based on metagenomic sequence data. Uncovering the complex microbiome community structure is essential to understanding the role of the microbiome in disease progression and susceptibility. Taxonomic abundance data generated from metagenomic sequencing technologies are high-dimensional and compositional, suffering from uneven sampling depth, over-dispersion, and zero-inflation. These characteristics often challenge the reliability of the current methods for microbiome community detection. To this end, we propose a Bayesian stochastic block model to study the microbiome co-occurrence network based on the recently developed modified centered-log ratio transformation tailored for microbiome data analysis. Our model allows us to incorporate taxonomic tree information using a Markov random field prior. The model parameters are jointly inferred by using Markov chain Monte Carlo sampling techniques. Our simulation study showed that the proposed approach performs better than competing methods even when taxonomic tree information is non-informative. We applied our approach to a real urinary microbiome dataset from postmenopausal women, the first time the urinary microbiome co-occurrence network structure has been studied. In summary, this statistical methodology provides a new tool for facilitating advanced microbiome studies.

The occurrence of extreme events like heavy precipitation or storms at a certain location often shows a clustering behaviour and is thus not described well by a Poisson process. We construct a general model for the inter-exceedance times in between such events which combines different candidate models for such behaviour. This allows us to distinguish data generating mechanisms leading to clusters of dependent events with exponential inter-exceedance times in between clusters from independent events with heavy-tailed inter-exceedance times, and even allows us to combine these two mechanisms for better descriptions of such occurrences. We investigate a modification of the Cram\'er-von Mises distance for the purpose of model fitting. An application to mid-latitude winter cyclones illustrates the usefulness of our work.

We study a class of Gaussian processes for which the posterior mean, for a particular choice of data, replicates a truncated Taylor expansion of any order. The data consist of derivative evaluations at the expansion point and the prior covariance kernel belongs to the class of Taylor kernels, which can be written in a certain power series form. We discuss and prove some results on maximum likelihood estimation of parameters of Taylor kernels. The proposed framework is a special case of Gaussian process regression based on data that is orthogonal in the reproducing kernel Hilbert space of the covariance kernel.

The mission of visual brain-computer interfaces (BCIs) is to enhance information transfer rate (ITR) to reach high speed towards real-life communication. Despite notable progress, noninvasive visual BCIs have encountered a plateau in ITRs, leaving it uncertain whether higher ITRs are achievable. In this study, we investigate the information rate limits of the primary visual channel to explore whether we can and how we should build visual BCI with higher information rate. Using information theory, we estimate a maximum achievable ITR of approximately 63 bits per second (bps) with a uniformly-distributed White Noise (WN) stimulus. Based on this discovery, we propose a broadband WN BCI approach that expands the utilization of stimulus bandwidth, in contrast to the current state-of-the-art visual BCI methods based on steady-state visual evoked potentials (SSVEPs). Through experimental validation, our broadband BCI outperforms the SSVEP BCI by an impressive margin of 7 bps, setting a new record of 50 bps. This achievement demonstrates the possibility of decoding 40 classes of noninvasive neural responses within a short duration of only 0.1 seconds. The information-theoretical framework introduced in this study provides valuable insights applicable to all sensory-evoked BCIs, making a significant step towards the development of next-generation human-machine interaction systems.

Early sensory systems in the brain rapidly adapt to fluctuating input statistics, which requires recurrent communication between neurons. Mechanistically, such recurrent communication is often indirect and mediated by local interneurons. In this work, we explore the computational benefits of mediating recurrent communication via interneurons compared with direct recurrent connections. To this end, we consider two mathematically tractable recurrent linear neural networks that statistically whiten their inputs -- one with direct recurrent connections and the other with interneurons that mediate recurrent communication. By analyzing the corresponding continuous synaptic dynamics and numerically simulating the networks, we show that the network with interneurons is more robust to initialization than the network with direct recurrent connections in the sense that the convergence time for the synaptic dynamics in the network with interneurons (resp. direct recurrent connections) scales logarithmically (resp. linearly) with the spectrum of their initialization. Our results suggest that interneurons are computationally useful for rapid adaptation to changing input statistics. Interestingly, the network with interneurons is an overparameterized solution of the whitening objective for the network with direct recurrent connections, so our results can be viewed as a recurrent linear neural network analogue of the implicit acceleration phenomenon observed in overparameterized feedforward linear neural networks.

Spiking Neural Networks (SNNs) have emerged as a hardware efficient architecture for classification tasks. The challenge of spike-based encoding has been the lack of a universal training mechanism performed entirely using spikes. There have been several attempts to adopt the powerful backpropagation (BP) technique used in non-spiking artificial neural networks (ANN): (1) SNNs can be trained by externally computed numerical gradients. (2) A major advancement towards native spike-based learning has been the use of approximate Backpropagation using spike-time dependent plasticity (STDP) with phased forward/backward passes. However, the transfer of information between such phases for gradient and weight update calculation necessitates external memory and computational access. This is a challenge for standard neuromorphic hardware implementations. In this paper, we propose a stochastic SNN based Back-Prop (SSNN-BP) algorithm that utilizes a composite neuron to simultaneously compute the forward pass activations and backward pass gradients explicitly with spikes. Although signed gradient values are a challenge for spike-based representation, we tackle this by splitting the gradient signal into positive and negative streams. We show that our method approaches BP ANN baseline with sufficiently long spike-trains. Finally, we show that the well-performing softmax cross-entropy loss function can be implemented through inhibitory lateral connections enforcing a Winner Take All (WTA) rule. Our SNN with a 2-layer network shows excellent generalization through comparable performance to ANNs with equivalent architecture and regularization parameters on static image datasets like MNIST, Fashion-MNIST, Extended MNIST, and temporally encoded image datasets like Neuromorphic MNIST datasets. Thus, SSNN-BP enables BP compatible with purely spike-based neuromorphic hardware.

This paper addresses the benefits of pooling data for shared learning in maintenance operations. We consider a set of systems subject to Poisson degradation that are coupled through an a-priori unknown rate. Decision problems involving these systems are high-dimensional Markov decision processes (MDPs). We present a decomposition result that reduces such an MDP to two-dimensional MDPs, enabling structural analyses and computations. We leverage this decomposition to demonstrate that pooling data can lead to significant cost reductions compared to not pooling.

The design of automatic speech pronunciation assessment can be categorized into closed and open response scenarios, each with strengths and limitations. A system with the ability to function in both scenarios can cater to diverse learning needs and provide a more precise and holistic assessment of pronunciation skills. In this study, we propose a Multi-task Pronunciation Assessment model called MultiPA. MultiPA provides an alternative to Kaldi-based systems in that it has simpler format requirements and better compatibility with other neural network models. Compared with previous open response systems, MultiPA provides a wider range of evaluations, encompassing assessments at both the sentence and word-level. Our experimental results show that MultiPA achieves comparable performance when working in closed response scenarios and maintains more robust performance when directly used for open responses.

Data-driven modeling is useful for reconstructing nonlinear dynamical systems when the underlying process is unknown or too expensive to compute. Having reliable uncertainty assessment of the forecast enables tools to be deployed to predict new scenarios unobserved before. In this work, we first extend parallel partial Gaussian processes for predicting the vector-valued transition function that links the observations between the current and next time points, and quantify the uncertainty of predictions by posterior sampling. Second, we show the equivalence between the dynamic mode decomposition and the maximum likelihood estimator of the linear mapping matrix in the linear state space model. The connection provides a data generating model of dynamic mode decomposition and thus, uncertainty of predictions can be obtained. Furthermore, we draw close connections between different data-driven models for approximating nonlinear dynamics, through a unified view of data generating models. We study two numerical examples, where the inputs of the dynamics are assumed to be known in the first example and the inputs are unknown in the second example. The examples indicate that uncertainty of forecast can be properly quantified, whereas model or input misspecification can degrade the accuracy of uncertainty quantification.

In large-scale systems there are fundamental challenges when centralised techniques are used for task allocation. The number of interactions is limited by resource constraints such as on computation, storage, and network communication. We can increase scalability by implementing the system as a distributed task-allocation system, sharing tasks across many agents. However, this also increases the resource cost of communications and synchronisation, and is difficult to scale. In this paper we present four algorithms to solve these problems. The combination of these algorithms enable each agent to improve their task allocation strategy through reinforcement learning, while changing how much they explore the system in response to how optimal they believe their current strategy is, given their past experience. We focus on distributed agent systems where the agents' behaviours are constrained by resource usage limits, limiting agents to local rather than system-wide knowledge. We evaluate these algorithms in a simulated environment where agents are given a task composed of multiple subtasks that must be allocated to other agents with differing capabilities, to then carry out those tasks. We also simulate real-life system effects such as networking instability. Our solution is shown to solve the task allocation problem to 6.7% of the theoretical optimal within the system configurations considered. It provides 5x better performance recovery over no-knowledge retention approaches when system connectivity is impacted, and is tested against systems up to 100 agents with less than a 9% impact on the algorithms' performance.